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Crystal structure of serine hydroxymethyltransferase from Burkholderia pseudomallei
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KKJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 289 PACT SCREEN CONDITION C6, 20% PEG 6000, 0.2 M NaCl, 0.1 M HEPES-KOH pH 7.0, 24.1 mg/mL protein, 0.4/0.4 uL drops, Crystal ID 109933C6, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.16 42.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.212 α = 97.79 b = 61.865 β = 89.97 c = 117.577 γ = 110.24
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 2008-08-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 0.99994 ALS 5.0.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.4 58.222 94.6 0.044 0.044 12.358 2.1 408650 190206
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.69 86.4 0.408 0.408 1.8 2.1 25383
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1KKJ 1.6 58.222 190195 9593 94.61 0.188 0.187 0.1938 0.206 0.2132 RANDOM 20.891
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -0.29 0.52 -0.09 1.13 0.24 -0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.731 r_dihedral_angle_4_deg 14.934 r_dihedral_angle_3_deg 13.699 r_dihedral_angle_1_deg 5.452 r_scangle_it 2.595 r_scbond_it 1.472 r_angle_other_deg 1.33 r_angle_refined_deg 1.2 r_mcangle_it 0.911 r_mcbond_it 0.476
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.731 r_dihedral_angle_4_deg 14.934 r_dihedral_angle_3_deg 13.699 r_dihedral_angle_1_deg 5.452 r_scangle_it 2.595 r_scbond_it 1.472 r_angle_other_deg 1.33 r_angle_refined_deg 1.2 r_mcangle_it 0.911 r_mcbond_it 0.476 r_mcbond_other 0.086 r_chiral_restr 0.058 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11605 Nucleic Acid Atoms Solvent Atoms 1607 Heterogen Atoms 24
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction